We describe and validate a volumetric three-dimensional registration method, and compare it to our previously validated two-dimensional/three-dimensional method. CT/MRI and SPECT data from 14 patients were interactively fused using a polynomial warping technique. Registration accuracy was confirmed visually and by a nonsignificant F value from multivariate analysis of the transformed landmarks, a significant difference of the squared sum of intensity differences between the transformed/untransformed and the reference volume both at the 0.05 (p > 0.05) confidence level and an average 31% improvement of the correlation coefficient and cross correlation. For the two-dimensional/three-dimensional method, ROI center-to-center distance ranged from 1.42 to 11.32 mm (for liver) with an average of 6.13 mm +/- 3.09 mm. The average ROI overlap was 92.51% with a 95% confidence interval of 90.20-96.88%. The new method is superior because it operates on the true three-dimensional volume. Both methods give good registration results, take 10 to 30 min, and require anatomic knowledge.